And yeah, Stark lifted him up some building to get a better vantage point and to pick off aliens... but he's only in one corner of one building rooftop so from there I think his ability to see the whole city would be limted. Why not put him on Stark tower.. not only can he still pick off guys...

Do you have any idea how high Stark Tower was? It's a modification of the MetLife Building just north of Grand Central Station, with a bunch of new floors added on top of it. The MetLife Building by itself is 59 stories and 808 feet high; the Stark-modified version is about 200 feet taller, rivalling the Chrysler Building in height. Hawkeye may have keen vision, but that's asking a little much. Not to mention that arrows wouldn't be particularly effective over such a great distance, particularly with the high winds you get at those altitudes.

Hawkeye could still take into effect the winds direction and still hit the mark.